Burning fuses does not matter if you don't plan to downgrade, so by all means, update your sysMMC via Nintendo's system update.
As for your emuMMC, this is where things are going to get complicated... Normally you wouldn't need to update your emuMMC but with 9.0 there was a game card reader update, so you will no longer be able to read cards on emuMMC unless you update.
You CAN use ChoiDujour to update your emuMMC but I advise you to take caution and backup your saves or anything else your care about, as plenty of people have been having loads of issues applying this update with ChoiDujour and ending up with an inaccessible emuMMC.
My recommendation is to just skip all that by:
- Backing up saves with Checkpoint
- Updating sysMMC via system update
- Getting all the latest Atmos files and Hekate
- Deleting emuMMC
- Creating fresh new emuMMC from updated sysMMC
- Restoring saves
This is what I typically do if I must update, except for game saves as I only use CFW for Homebrew but I've successfully avoided any of the headaches people are giving themselves doing it this way. If you use any Homebrew you'll need to update to the latest Atmos for buttons to work due to changes with libnx. There is a temporary fix implemented until all Homebrew has be recompiled.
Oh, I assume you'll also be needing sigpatches as well since you mentioned them. There's a new pack of them you'll need to grab.
Proceed how you wish but backup what your cherish.
